There are all sorts of instructions for the mod, LAA, MultiSH4, etc. on the first page of this thread. There are all sorts of instructions for the same on the download page, plus there are all sorts of instructions in the mod's Support folder, including a TOC pdf that will load most any of them. The most thorough instructions are in the mod's Support folder. What you have now succeeded in doing is to trash not only your FotRSU Save games, but now that you've saved into the same folder with FotRSU active, you have now most likely trashed the Saves for Dark Waters. Neither mod will function correctly. To put it simply, there are different configurations for ships "calls" for them to show in the game, where OM might use a given ship with a Type=3 and FotRSU might use Type=2. Or, the same ship might have a different "name", or a different "ClassName" - which is not the same as "name"... not to confuse the issue.
If you know which saves that show on the Save menu are for FotRSU, then I would delete all of those. De-activate FotRSU, and then hope you can still use your Atlantic Saves after you re-activate Dark Waters. You cannot mix stock with Dark Waters with FotRSU with TMO, etc. ad infinitum ad nauseum.
Look for the "Install Notes For the Various Versions of SH4 in Windows.pdf" file in the Support folder, and on Page 11, "Digging Deeper", are some comments on using MultiSH4. Basically, you make a copy of your "clean" Stock game folder, and paste it somewhere else, rename it, and use MultiSH4 inside that new copy of the game folder to create a new Save folder, such as "FRS" or "ODW" or whatever you want to use (only 3 characters). So the Stock game then uses the SH4 folder, your 2nd copy with Dark Waters activated would use the "ODW" folder, and the 3rd copy of the game with FotRSU activated would use the "FRS" folder, etc.
Edit: Potoroo's MultiSH4 - it is assumed you know what it is...
Potoroo's MultiSH3 - has basic instructions, and very similar to SH4 procedure.
Webster's How to make multiple sh4 installs
Which is linked to from THEBERBSTER's
SH4 <> TUTORIALS <> HOW TO DO IT <> INFO <> DOWNLOAD LINKS -STICKY INDEX thread. Lots of reading material for you.